NM_181501.2:c.773+1937T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_181501.2(ITGA1):​c.773+1937T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,094 control chromosomes in the GnomAD database, including 3,120 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.20 ( 3120 hom., cov: 32)

Consequence

ITGA1
NM_181501.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.151

Publications

9 publications found
Variant links:
Genes affected
ITGA1 (HGNC:6134): (integrin subunit alpha 1) This gene encodes the alpha 1 subunit of integrin receptors. This protein heterodimerizes with the beta 1 subunit to form a cell-surface receptor for collagen and laminin. The heterodimeric receptor is involved in cell-cell adhesion and may play a role in inflammation and fibrosis. The alpha 1 subunit contains an inserted (I) von Willebrand factor type I domain which is thought to be involved in collagen binding. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ITGA1NM_181501.2 linkc.773+1937T>C intron_variant Intron 7 of 28 ENST00000282588.7 NP_852478.1 P56199

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ITGA1ENST00000282588.7 linkc.773+1937T>C intron_variant Intron 7 of 28 1 NM_181501.2 ENSP00000282588.5 P56199
ITGA1ENST00000513737.5 linkn.524+1937T>C intron_variant Intron 5 of 5 5
ITGA1ENST00000650673.1 linkn.773+1937T>C intron_variant Intron 7 of 28 ENSP00000498529.1 A0A494C0F7

Frequencies

GnomAD3 genomes
AF:
0.197
AC:
29996
AN:
151974
Hom.:
3108
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.216
Gnomad AMI
AF:
0.150
Gnomad AMR
AF:
0.138
Gnomad ASJ
AF:
0.181
Gnomad EAS
AF:
0.249
Gnomad SAS
AF:
0.280
Gnomad FIN
AF:
0.157
Gnomad MID
AF:
0.197
Gnomad NFE
AF:
0.198
Gnomad OTH
AF:
0.179
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.198
AC:
30049
AN:
152094
Hom.:
3120
Cov.:
32
AF XY:
0.195
AC XY:
14521
AN XY:
74354
show subpopulations
African (AFR)
AF:
0.217
AC:
9004
AN:
41484
American (AMR)
AF:
0.138
AC:
2106
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
0.181
AC:
630
AN:
3472
East Asian (EAS)
AF:
0.251
AC:
1295
AN:
5168
South Asian (SAS)
AF:
0.278
AC:
1341
AN:
4820
European-Finnish (FIN)
AF:
0.157
AC:
1665
AN:
10590
Middle Eastern (MID)
AF:
0.190
AC:
56
AN:
294
European-Non Finnish (NFE)
AF:
0.198
AC:
13433
AN:
67972
Other (OTH)
AF:
0.181
AC:
382
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1228
2456
3684
4912
6140
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
330
660
990
1320
1650
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.201
Hom.:
5055
Bravo
AF:
0.195
Asia WGS
AF:
0.247
AC:
858
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
6.1
DANN
Benign
0.72
PhyloP100
0.15
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs2456203; hg19: chr5-52179790; API